<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Guys,<div><br></div><div>I have a molecule with a nitrogen bonded to three carbons and one proton. Can anyone tell me what parameters to use? I have looked through the amber parameter file and can't find suitable parameters. I'm not sure if it is probable, but if the N1 of cytidine were protonated, it would be similar to my situation. </div><div><br></div><div>Many thanks,</div><div><br></div><div>Sam</div><div><br></div><div><br></div><div><br><div><html>On Sep 26, 2007, at 3:27 AM, <a href="mailto:janne.hirvi@joensuu.fi">janne.hirvi@joensuu.fi</a> wrote:</html><br class="Apple-interchange-newline"><blockquote type="cite">Thanks for your help Alan, Yang, and Belquis!<br><br>Now I managed to get trajectory in which a droplet stays in the middle of the simulation box while a surface moves below the droplet. First I used trjconv to remove periodicity (-pbc nojump) and then performed translational fit for the droplet (-fit translational) and finally transferred all the translating surface atoms back to the simulation box (-pbc -inbox).<br><br>However, there is still a problem with fitting procedure which is performed in three dimension and hence the surface translates upwards during the video. It should be quite easy to modify trjconv so that the fitting is performed only for the xy coordinates (not for the z coordinate perpendicular to the surface) but with my programming skills I wasn't able to do that (actually I wasnt able to find the correct lines). So I would like to know if someone has made a such modification to trjconv (trjconv_d) or could help me to do it?<br><br>Thanks,<br><br>Janne<br><br><br><blockquote type="cite">Hello Janne,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">this is what I usually do when my molecules cross the box or dance all<br></blockquote><blockquote type="cite">around and it works for me:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I first do this with the "original" unmodified or fitted xtc or trr file:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">trjconv -f -o -pbc nojump<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">then i take the modified trr or xtc and do a fit:<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">trjconv -f -s -fit rot+trans<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Belquis<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite">Hello gmx-users!<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">I am trying to make a simulation video in which a water droplet is<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">rolling or sliding on a surface. Due to a periodic boundary conditions<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">a droplet is not whole all the time but it disappears from the right<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">and appears from the left in cycles.<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">I think that I could create more visual video by removing the lateral<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">motion of the center of mass of a droplet so that the droplet would<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">stay whole<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">in the middle of simulation window and the surface would translate<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">below the droplet. I am not exactly sure how realistic this kind of<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">video would be and would like to know if someone has better ideas?<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">If there are no better ideas I would need advices to be able to create<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">a such trajectory or video. Right now I am struggling with trjconv<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">which might be suitable for this purpose. However, if I use the<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">droplet as a group for translational fit (-fit translation) I get<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">trajectory in which the whole system wanders strangly (laterally (the<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">surface moves first to the left and then back to the right) and also<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">in perpendicular to the surface due to the lowering of the height of<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">the center of mass of the droplet during the simulation) and the<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">droplet wont stay whole in the middle of the box. Any ideas what I am<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">doing wrong or how I would be able to get rid of even this lateral<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">wandering so that I could at least see how realistic this procedure is?<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Thanks for your time and help in advance,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Janne<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">------------------------------------------------------------------------------<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Janne Hirvi, MSc(Physical Chemistry), Researcher<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">University of Joensuu, Department of Chemistry, P.O.Box 111 80101 Joensuu,<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">FI<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Tel: +358 13 2514544 & +358 50 3474223<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">E-mail: <a href="mailto:Janne.Hirvi@joensuu.fi">Janne.Hirvi@joensuu.fi</a> & <a href="mailto:hirvi@cc.joensuu.fi">hirvi@cc.joensuu.fi</a><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">------------------------------------------------------------------------------<br></blockquote></blockquote>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at http://www.gromacs.org/search before posting!<br>Please don't post (un)subscribe requests to the list. 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